sokrypton / sokrypton/ColabFold

Can't run pdbfixer

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Description

Expected Behavior

Hello !
I installed pdbfixer with conda. There was no error.

Current Behavior

When trying to run pdbfixer with the command line: " pdbfixer ", I get these errors :
"
Traceback (most recent call last):
File "/home/ikram/miniconda3/bin/pdbfixer", line 6, in
from pdbfixer.pdbfixer import main
File "/home/ikram/miniconda3/lib/python3.8/site-packages/pdbfixer/init.py", line 2, in
from .pdbfixer import PDBFixer
File "/home/ikram/miniconda3/lib/python3.8/site-packages/pdbfixer/pdbfixer.py", line 35, in
import openmm as mm
File "/home/ikram/miniconda3/lib/python3.8/site-packages/openmm/init.py", line 24, in
from openmm.openmm import *
File "/home/ikram/miniconda3/lib/python3.8/site-packages/openmm/openmm.py", line 10, in
from . import _openmm
ImportError: /home/ikram/miniconda3/lib/python3.8/site-packages/openmm/../../../libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/ikram/miniconda3/lib/python3.8/site-packages/openmm/../../../libOpenMM.so.8.0)
"

Steps to Reproduce (for bugs)

Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally ypdate you local installation colabfold_batch to the newest version.
Please provide your input if you can share it.

ColabFold Output (for bugs)

Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.

Context

Providing context helps us come up with a solution and improve our documentation for the future.

Your Environment

Include as many relevant details about the environment you experienced the bug in.

  • Git commit used
  • If you run it on a local system. Please add the server specifications
  • Operating system and version:

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with the reported import traceback and inspect the project's packaging or dependency configuration for the pdbfixer and OpenMM installation path. Reproduce the failure in the reported conda/Python 3.8 environment; done means the pdbfixer command starts without the GLIBCXX_3.4.30 ImportError.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics, cli
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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